The First Minister had invited the Prime Minister to discuss the Covid response while he visits Scotland this week.
Now Mr Johnson has insisted he had not “snubbed” the chance to meet with Ms Sturgeon, and thanked the Scottish Government for their work on the vaccination rollout.
He said: “No, I haven’t. I’m always delighted, always, always, always, delighted – and look, we, seriously, we work together.
“The Government of the UK, the Scottish Government, at all levels work together on the things that matter to the people of our country, particularly rolling out vaccinations, and, generally, making sure that we bounce back and build back better from the pandemic, and we are going to continue.
“I thank the Scottish Government for what they’ve been doing, a really high rate of vaccination here in Scotland, and really fantastic achievement by the people of Scotland coming forward to get vaccinated – working with them to finish that – but also making sure that we have a very strong economic recovery, and I think the country is well-placed to do that.”
Mr Johnson had earlier written to the First Minister and claimed while he was keen to talk about joint plans for the vaccination roll-out and the recovery from the pandemic, he wanted to do so in a “structured forum” between the UK government and the leaders of all the devolved parliaments.
He added: “I understand our officials have made good progress on the details of this since we last spoke.
"The UK government is working closely with the devolved Scottish government on a variety of different issues. I look forward to meeting with you soon and working together in the interests of people in all parts of our country."
Ms Sturgeon labelled the decision a “missed opportunity”.
She told broadcasters: “I don’t feel snubbed. I think most people will think it’s a bit odd, and a bit strange, that we’ve got a Prime Minister visiting Scotland who talks a lot, rightly, about the need – despite our political differences – for us to work together where we can on getting through Covid and into Covid recovery but doesn’t take the opportunity when in Scotland to come and talk to me directly about how we might co-operate and work together.
“I think people will just find that strange and it’s for Boris Johnson to explain, I suppose, why.
“This would be the first opportunity, given Covid, for us to sit down, appropriately socially distanced and have a face-to-face chat. I think it would have been a good opportunity.
“There’s lots that Boris Johnson and I fundamentally disagree on but we both lead governments that are trying to get our countries through Covid and so there’s a lot for us to co-operate on.
“So, you know, missed opportunity but that’s on him. I stand ready to work with whoever, however I can to get Scotland through Covid and into recovery.”
Mr Johnson also used the visit to insist he was “totally committed” to funding the high numbers of police officers needed for the Cop26 summit in Glasgow this November.
The Prime Minister added he would aim to “backfill” police officers brought in from around the UK.
He said: “We are totally committed to funding the police and to making sure that they have the resources that they need to do what’s necessary. We think that there’ll be about 10,000 a day.
“They’ll be, of course, supported throughout the summit – which will go on for many days – by about 7,000 officers from around the UK.
“It’s also very important that we have backfilling around the whole of the UK and we don’t have a situation in which all the officers from around the country are sucked into one big operation.
“We’ve got to make sure that policing takes place normally throughout the whole of the UK during the Cop26 summit in November, so we’ll be putting all the money that’s needed to make sure that happens.”